Arrays of chemical binding agents, such as nucleic acids and polypeptides, have become an increasingly important tool in the biotechnology industry and related fields. These chemical (i.e., binding agent or ligand) arrays, in which a plurality of chemical binding agents are positioned on a solid support surface in the form of an array or pattern, find use in a variety of applications, including gene expression analysis, drug screening, nucleic acid sequencing, mutation analysis, comparative genome hybridization, location analysis and the like.